[WIP] Documentation, Test cases and CI for trx_file_memmap

.github/workflows/python-package.yml

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+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: Python package
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.7", "3.8", "3.9"]
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install flake8 pytest pytest-cov
+        python -m pip install .
+    - name: Lint with flake8
+      run: |
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+    - name: Test with pytest
+      run: |
+        pytest trx_file_memmap/tests

trx_file_memmap/tests/data/small_fldr.trx/dpg/AF_L/mean_fa.float16

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+�5

trx_file_memmap/tests/data/small_fldr.trx/dpg/AF_R/mean_fa.float16

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+�5

trx_file_memmap/tests/data/small_fldr.trx/dpg/CC/mean_fa.float16

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+�5

trx_file_memmap/tests/data/small_fldr.trx/dps/algo.uint8

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+










































































































































































trx_file_memmap/tests/data/small_fldr.trx/header.json

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+{"DIMENSIONS": [117, 151, 115], "NB_STREAMLINES": 1000, "NB_VERTICES": 33886, "VOXEL_TO_RASMM": [[-1.25, 0.0, 0.0, 72.5], [0.0, 1.25, 0.0, -109.75], [0.0, 0.0, 1.25, -64.5], [0.0, 0.0, 0.0, 1.0]]}

trx_file_memmap/tests/test_memmap.py

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+#!/usr/bin/env python
+from numpy.ma.core import shape
+import pytest
+import numpy as np
+import trx_file_memmap.trx_file_memmap as tmm
+
+from tempfile import mkdtemp
+import os.path as path
+
+
+@pytest.mark.parametrize(
+    "arr,expected,value_error",
+    [
+        (np.ones((5, 5, 5), dtype=np.int16), None, True),
+        (np.ones((5, 4), dtype=np.int16), "mean_fa.4.int16", False),
+        (np.ones((5, 4), dtype=np.float64), "mean_fa.4.float64", False),
+        (np.ones((5, 1), dtype=np.float64), "mean_fa.float64", False),
+        (np.ones((1), dtype=np.float64), "mean_fa.float64", False),
+    ],
+)
+def test__generate_filename_from_data(
+    arr, expected, value_error, filename="mean_fa.bit"
+):
+
+    if value_error:
+        with pytest.raises(ValueError):
+            new_fn = tmm._generate_filename_from_data(arr=arr, filename=filename)
+            assert new_fn is None
+    else:
+        new_fn = tmm._generate_filename_from_data(arr=arr, filename=filename)
+        assert new_fn == expected
+
+
+@pytest.mark.parametrize(
+    "filename,expected,value_error",
+    [
+        ("mean_fa.float64", ("mean_fa", 1, ".float64"), False),
+        ("mean_fa.5.int32", ("mean_fa", 5, ".int32"), False),
+        ("mean_fa", None, True),
+        ("mean_fa.5.4.int32", None, True),
+        pytest.param(
+            "mean_fa.fa", None, True, marks=pytest.mark.xfail, id="invalid extension"
+        ),
+    ],
+)
+def test__split_ext_with_dimensionality(filename, expected, value_error):
+    if value_error:
+        with pytest.raises(ValueError):
+            assert tmm._split_ext_with_dimensionality(filename) == expected
+    else:
+        assert tmm._split_ext_with_dimensionality(filename) == expected
+
+
+@pytest.mark.parametrize(
+    "offsets,nb_vertices,expected",
+    [
+        (np.array(range(5), dtype=np.int16), 4, np.array([1, 1, 1, 1, 0])),
+        (np.array([0, 1, 0, 3, 4], dtype=np.int16), 4, np.array([1, 3, 0, 1, 0])),
+        (np.array(range(4), dtype=np.int16), 4, np.array([1, 1, 1, 1])),
+    ],
+)
+def test__compute_lengths(offsets, nb_vertices, expected):
+
+    lengths = tmm._compute_lengths(offsets=offsets, nb_vertices=nb_vertices)
+    assert np.array_equal(lengths, expected)
+
+
+@pytest.mark.parametrize(
+    "ext,expected",
+    [
+        (".bit", True),
+        (".int16", True),
+        (".float32", True),
+        (".ushort", True),
+        (".txt", False),
+    ],
+)
+def test__is_dtype_valid(ext, expected):
+    assert tmm._is_dtype_valid(ext) == expected
+
+
+@pytest.mark.parametrize(
+    "arr,l_bound,r_bound,expected",
+    [
+        (np.array(range(5), dtype=np.int16), None, None, 4),
+        (np.array([0, 1, 0, 3, 4], dtype=np.int16), None, None, 1),
+        (np.array([0, 1, 2, 0, 4], dtype=np.int16), None, None, 2),
+        (np.array(range(5), dtype=np.int16), 1, 2, 2),
+        (np.array(range(5), dtype=np.int16), 3, 3, 3),
+        (np.zeros((5), dtype=np.int16), 3, 3, -1),
+    ],
+)
+def test__dichotomic_search(arr, l_bound, r_bound, expected):
+    end_idx = tmm._dichotomic_search(arr, l_bound=l_bound, r_bound=r_bound)
+    assert end_idx == expected
+
+
+@pytest.mark.parametrize(
+    "basename, create, expected",
+    [
+        ("offsets.int16", True, np.array(range(12), dtype=np.int16).reshape((3, 4))),
+        ("offsets.float32", False, None),
+    ],
+)
+def test__create_memmap(basename, create, expected):
+    if create:
+        # Need to create array before evaluating
+        filename = path.join(mkdtemp(), basename)
+        fp = np.memmap(filename, dtype=np.int16, mode="w+", shape=(3, 4))
+        fp[:] = expected[:]
+        mmarr = tmm._create_memmap(filename=filename, shape=(3, 4), dtype=np.int16)
+        assert np.array_equal(mmarr, expected)
+
+    else:
+        mmarr = tmm._create_memmap(filename=basename, shape=(0,), dtype=np.int16)
+        assert path.isfile(basename)
+        assert np.array_equal(mmarr, np.zeros(shape=(0,), dtype=np.float32))
+
+
+# need dpg test with missing keys
+@pytest.mark.parametrize(
+    "path,check_dpg,value_error",
+    [
+        ("trx_file_memmap/tests/data/small_compressed.trx", False, False),
+        ("trx_file_memmap/tests/data/small.trx", True, False),
+        ("trx_file_memmap/tests/data/small_fldr.trx", False, False),
+        ("trx_file_memmap/tests/data/dontexist.trx", False, True),
+    ],
+)
+def test__load(path, check_dpg, value_error):
+
+    # Need to perhaps improve test
+    if value_error:
+        with pytest.raises(ValueError):
+            assert not isinstance(
+                tmm.load(input_obj=path, check_dpg=check_dpg), tmm.TrxFile
+            )
+    else:
+        assert isinstance(tmm.load(input_obj=path, check_dpg=check_dpg), tmm.TrxFile)
+
+
+@pytest.mark.parametrize(
+    "path",
+    [
+        ("trx_file_memmap/tests/data/small.trx"),
+    ],
+)
+def test_load_zip(path):
+    assert isinstance(tmm.load_from_zip(path), tmm.TrxFile)
+
+
+@pytest.mark.parametrize("path", [("trx_file_memmap/tests/data/small_fldr.trx")])
+def test_load_directory(path):
+    assert isinstance(tmm.load_from_directory(path), tmm.TrxFile)
+
+
+def test_concatenate():
+    pass
+
+
+def test_save():
+    pass
+
+
+def test_zip_from_folder():
+    pass
+
+
+def test_trxfile_init():
+    pass
+
+
+def test_trxfile_print():
+    pass
+
+
+def test_trxfile_len():
+    pass
+
+
+def test_trxfile_getitem():
+    pass
+
+
+def test_trxfile_deepcopy():
+    pass
+
+
+def test_get_real_len():
+    pass
+
+
+def test_copy_fixed_arrays_from():
+    pass
+
+
+def test_initialize_empty_trx():
+    pass
+
+
+def test_create_trx_from_pointer():
+    pass
+
+
+def test_trxfile_resize():
+    pass
+
+
+def test_trxfile_append():
+    pass
+
+
+def test_trxfile_getgroup():
+    pass
+
+
+def test_trxfile_select():
+    pass
+
+
+def test_trxfile_to_memory():
+    pass
+
+
+def test_trxfile_close():
+    pass